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Coenzyme and cofactor metabolism belongs to biochemical processes significantly regulated in human granulosa cells collected after IVF during long-term primary in vitro culture

Mariusz J. Nawrocki
Mariusz J. Nawrocki
, 
Rafał Sibiak
Rafał Sibiak
, 
Maciej Brązert
Maciej Brązert
, 
Piotr Celichowski
Piotr Celichowski
, 
Leszek Pawelczyk
Leszek Pawelczyk
, 
Błażej Chermuła
Błażej Chermuła
, 
Claudia Dompe
Claudia Dompe
, 
Bartosz Kempisty
Bartosz Kempisty
 and 
Paul Mozdziak
Paul Mozdziak
   | Dec 21, 2019
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Published Online: Dec 21, 2019
Page range: 152 - 160
Received: Oct 22, 2019
Accepted: Nov 26, 2019
DOI: https://doi.org/10.2478/acb-2019-0021
Keywords
© 2019 Mariusz J. Nawrocki, Rafał Sibiak, Maciej Brązert, Piotr Celichowski, Leszek Pawelczyk, Błażej Chermuła, Claudia Dompe, Bartosz Kempisty, Paul Mozdziak, published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Figure 1

Heat map representation of differentially expressed genes belonging to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. Arbitrary signal intensity acquired from microarray analysis is represented by colours (green higher expression; red lower expression). Log2 signal intensity values for any single gene were resized to Row Z-Score scale (from -2, the lowest expression to +2, the highest expression for single gene)
Heat map representation of differentially expressed genes belonging to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. Arbitrary signal intensity acquired from microarray analysis is represented by colours (green higher expression; red lower expression). Log2 signal intensity values for any single gene were resized to Row Z-Score scale (from -2, the lowest expression to +2, the highest expression for single gene)

Figure 2

Circular visualization of the results of gene-annotation enrichment analysis. The outer circle shows a scatter plot for each term of the logFC of the assigned genes. Green dots display up- regulation and red ones down- regulation. The inner circle is the representation of z-score. The width of the bar represents the number of genes that are present in the GO term and the color represents the z-score
Circular visualization of the results of gene-annotation enrichment analysis. The outer circle shows a scatter plot for each term of the logFC of the assigned genes. Green dots display up- regulation and red ones down- regulation. The inner circle is the representation of z-score. The width of the bar represents the number of genes that are present in the GO term and the color represents the z-score

Figure 3

Representation of the mutual relationship between differently expressed genes that belong to 10 chosen genes from “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The ribbons indicate which gene belongs to which category. The middle circle shows the logarithm of the fold change (LogFC) between D7/D1, D15/D1 and D30/D1 respectively. The color of each block corresponds to the LogFC of each gene (green – upregulated, red – downregulated). The genes were sorted by LogFC from most to least changed gene
Representation of the mutual relationship between differently expressed genes that belong to 10 chosen genes from “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The ribbons indicate which gene belongs to which category. The middle circle shows the logarithm of the fold change (LogFC) between D7/D1, D15/D1 and D30/D1 respectively. The color of each block corresponds to the LogFC of each gene (green – upregulated, red – downregulated). The genes were sorted by LogFC from most to least changed gene

Figure 4

Heatmap showing the gene occurrence between the chosen 10 differently expressed genes that belong to “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The yellow color is associated with gene occurrence in the GO Term. The intensity of the color corresponds to the amount of GO BP terms that each gene belongs to
Heatmap showing the gene occurrence between the chosen 10 differently expressed genes that belong to “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The yellow color is associated with gene occurrence in the GO Term. The intensity of the color corresponds to the amount of GO BP terms that each gene belongs to

Figure 5

STRING-generated interaction network among 10 most downregulated genes belonging to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The intensity of the edges reflects the strength of the interaction scores
STRING-generated interaction network among 10 most downregulated genes belonging to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. The intensity of the edges reflects the strength of the interaction scores

Figure 6

Functional interaction (FI) between differently expressed genes that belong to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. In the following figure “->” stands for activating/catalyzing, “-|” for inhibiting, “-” for FIs extracted from complexes or inputs, and “---” for predicted FIs
Functional interaction (FI) between differently expressed genes that belong to the “coenzyme biosynthetic process”, “coenzyme metabolic process”, “cofactor biosynthetic process” and “cofactor metabolic process” GO BP terms. In the following figure “->” stands for activating/catalyzing, “-|” for inhibiting, “-” for FIs extracted from complexes or inputs, and “---” for predicted FIs

Gene symbols, fold change in expression ratio, Entrez gene IDs, corrected p values and mean value of fold change ratio of the 10 chosen differentially expressed, studied genes

GENE SYMBOLRATIO D7/D1RATIO D15/D1RATIO D30/D1ADJUSTED P.VALUE D7/D1ADJUSTED P.VALUE D15/D1ADJUSTED P.VALUE D30/D1ENTREZ GENE IDMEAN RATIO
ELOVL5-9,251267471-9,938010711-10,388033850,7720634450,0014100110,00122111860481-9,85910401
GPAM-8,02377638-8,20961524-10,826714420,0768453340,0011940580,00113500357678-9,020035348
KYNU-7,126693786-8,012261249-10,126837530,0468569130,0005998850,0004922348942-8,421930854
SCD-7,317544673-7,853658138-7,577633430,8977898770,010645490,0082923586319-7,582945414
MTHFD2L-6,467890961-8,066798079-7,4689773840,7261936450,0059718850,003885481441024-7,334555475
NAMPT-7,606632986-5,292293151-7,4229382440,1554309350,0045190680,00757106610135-6,773954794
HMGCR-5,271754338-7,924819598-5,8873631840,2210163130,0098717550,0044419243156-6,361312373
ELOVL6-4,519000381-5,545912723-5,5464992450,9997945410,0772158340,0479424779071-5,203804116
TPK1-2,907857277-6,352044342-4,3618217550,1047343370,0278165550,00461100427010-4,540574458
ME2-3,286963496-3,973472161-5,4420131880,0196766850,0026209290,0015699714200-4,234149615
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